A modular tool to aggregate results from bioinformatics analyses across many samples into a single report.
Report
generated on 2025-10-23, 13:46 UTC
based on data in:
/home/runner/work/pmultiqc/pmultiqc/data
pmultiqc
pmultiqc is a MultiQC module to show the pipeline performance of mass spectrometry based quantification pipelines such as nf-core/quantms, MaxQuant, and DIA-NN.URL: https://github.com/bigbio/pmultiqc
Results Overview
Summary Table
This table shows the summary statistics of the submitted data.
This table shows the summary statistics of the submitted data.
Showing 1/1 rows and 4/4 columns.
| #MS2 Spectra | #Identified MS2 Spectra | %Identified MS2 Spectra | #Peptides Identified | #Proteins Identified |
|---|---|---|---|---|
| 128230 | 20518 | 16.00% | 1523 | 185 |
HeatMap
This heatmap provides an overview of the performance of quantms.
This plot shows the pipeline performance overview.
Created with MultiQC
Pipeline Result Statistics
This plot shows the submitted results
This plot shows the submitted results.
Including the number of identified peptides and the number of identified modified peptides in the submitted results.
You can also remove the decoy with the `remove_decoy` parameter.
Showing 3/3 rows and 4/4 columns.
| Spectra File | #Peptide IDs | #Unambiguous Peptide IDs | #Modified Peptide IDs | #Protein (group) IDs |
|---|---|---|---|---|
| F001234 | 1788 | 1788 | 706 | 146 |
| F001235 | 1351 | 1351 | 627 | 130 |
| F001236 | 1034 | 1034 | 543 | 99 |
Identification Summary
Number of Peptides identified Per Protein
This plot shows the number of peptides per protein in the submitted data
Proteins supported by more peptide identifications can constitute more confident results.
MS2 and Spectral Stats
Number of Peaks per MS/MS spectrum
Histogram of number of peaks per MS/MS spectrum.
Too few peaks may indicate poor fragmentation; many peaks could indicate noisy spectra.
Peak Intensity Distribution
Histogram of ion intensity vs. frequency for all MS2 spectra.
High number of low intensity noise peaks expected; disproportionate high signal peaks may indicate issues.
Distribution of Precursor Charges
Bar chart of precursor ion charge distribution.
Use to identify potential ionization problems or unexpected distributions.
MS/MS Counts Per 3D-peak
An oversampled 3D-peak is defined as a peak whose peptide ion
(same sequence and same charge state) was identified by at least two distinct MS2 spectra
in the same Raw file.
For high complexity samples, oversampling of individual 3D-peaks automatically leads to
undersampling or even omission of other 3D-peaks, reducing the number of identified peptides.
Oversampling occurs in low-complexity samples or long LC gradients, as well as undersized dynamic
exclusion windows for data independent acquisitions.
